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| − | [[Category:Help]] | + | [[Category:Essentials]] |
| − | {|align=right
| + | Welcome to UF Research Computing! This page is intended to help new clients getting started on HiPerGator use. |
| − | |__TOC__
| |
| − | |}
| |
| − | Welcome to UF Research Computing! This page is intended to help new clients get started on HiPerGator. | |
| | | | |
| − | =From Zero to 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. |
| − | ==Initial Consult==
| |
| − | 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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| | | | |
| − | ==HiPerGator Accounts==
| |
| − | 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.
| + | =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]. |
| | | | |
| − | ==Trial Allocation==
| |
| − | We recommend that the group's sponsor [https://gravity.rc.ufl.edu/access/request-trial-allocation/ requests 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==
| + | For the initial interview we recommend prospective users to be ready to answer questions such as: |
| − | 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.
| |
| | | | |
| − | 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.
| + | * 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? |
| | | | |
| − | 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.
| + | ===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. |
| | | | |
| − | '''At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.'''
| + | ====User Account Creation==== |
| | + | 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. |
| | | | |
| − | =Introduction to Using HiPerGator= | + | ====Joining a Group==== |
| | + | 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). |
| | | | |
| − | ;Note: see a short [[Quick Start Guide]] for some hints on getting going and avoiding common pitfalls.
| + | [https://support.rc.ufl.edu 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. |
| | | | |
| − | To use HiPerGator or HiPerGator-AI you need three basic parts
| + | ===Trial Allocation=== |
| − | * Interfaces
| + | 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. |
| − | 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 [[JupyterHub]] or [[Open OnDemand]], but mostly you use a command-line Terminal interface through SSH connections (see below).
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| − | * 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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| − | *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]], [[JupyterHub], and [[Galaxy]] can manage job scheduling behind the scenes and may be more convenient than job submission from the command-line when appropriate. | |
| | | | |
| − | ==Interfaces== | + | ===Purchasing Resources=== |
| − | ===Connecting to a HiPerGator Terminal via SSH=== | + | 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. |
| − | 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]], [[Open_OnDemand|Open OnDemand]], or [[JupyterHub]].
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| | | | |
| − | Note that the UF security requirements include the use of [[Authentication_With_MFA|Multi-Factor Authentication]] when connecting to HiPerGator. See the [[SSH Multiplexing]] help if you are connecting from Linux or MacOS to reduce the frequency of MFA use.
| + | 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. |
| | | | |
| − | For any given command below, <code><username></code> should be replaced with the UFRC username (same as your GatorLink username).
| + | 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. |
| | | | |
| − | ====Connecting from Windows====
| + | '''At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.''' |
| − | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
| |
| − | ''Expand this section to view instructions for logging in with Windows.'' | |
| − | <div class="mw-collapsible-content" style="padding: 5px;">
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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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| − | | |
| − | For University-managed computers [http://www.chiark.greenend.org.uk/~sgtatham/putty PuTTY], [https://tabby.sh/ Tabby], and [https://gitforwindows.org/ Git Bash] are approved for 'fast track' installations.
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| | | | |
| − | '''PuTTY'''
| + | =Using HiPerGator= |
| − | * [http://www.chiark.greenend.org.uk/~sgtatham/putty Download PuTTY] to your local machine and start the program. | + | To use HiPerGator or HiPerGator-AI you must have basic understanding the following concepts: |
| − | * Connect to hpg.rc.ufl.edu. | + | * Use the various [[HPG Interfaces]] to connect to the system. |
| − | * At the login prompt, enter your username (this should be the same as your GatorLink username) | + | * See [[HPG Computation]] for an overview of running analyses on HiPerGator. |
| − | * Enter your password when prompted. You are now connected and ready to work!
| + | * 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]]. |
| | | | |
| − | '''Tabby''' | + | Click on the buttons below to explore. |
| − | * [https://github.com/Eugeny/tabby/releases/latest Download Tabby] to your local machine: tabby-version#-setup.exe or tabby-version#-portable.zip for a portable version.
| + | <div style = 'text-align: center;'> |
| − | * Star the program and click Settings > Profiles > +New profile > SSH connection
| + | [[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]] |
| − | Name: HiPerGator
| + | [[Image:Computation.png|frameless|upright=1|link=HPG Computation]] |
| − | Host: hpg.rc.ufl.edu
| + | [[Image:Scheduling.png|frameless|upright=1|link=HPG Scheduling]] |
| − | Username: <username>
| + | [[Image:Storage.png|frameless|upright=1|link=HPG Data Management]] |
| − | Password: "Set password" or "Add a private key"
| |
| − | * Click "Save"
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| − | * Click on the window icon "New tab with profile" and select "HiPerGator hpg.rc.ufl.edu"
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| − | * You are now connected and ready to work!
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| | </div> | | </div> |
| − | </div>
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| − |
| |
| − | ====Connecting from Linux and MacOS====
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| − | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
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| − | ''Expand to view instructions for connecting from Linux or MacOS.''
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| − | <div class="mw-collapsible-content" style="padding: 5px;">
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| − | You may omit GatorLinkUsername if the username on your local computer matches your GatorLink username e.g.
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| − |
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| − | Open a terminal and run
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| − | $ ssh <GatorLink Username>@hpg.rc.ufl.edu
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| − | or
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| − | $ ssh hpg.rc.ufl.edu
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| − |
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| − | Enter your password when the prompt appears. You are now connected to a login node and your working directory will be <code>/home/<GatorLink></code>, ready to work!
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| − | </div>
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| − | </div>
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| − |
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| − | ===Logging in via web browser===
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| − | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
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| − | ''Expand to view instructions for Logging in via web browser.''
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| − | <div class="mw-collapsible-content" style="padding: 5px;">
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| − | * Services like OpenOnDemand (OOD) and JupyterHub require the users to be on the UF network. If the user is off the campus network they need to be connected to the UF [https://it.ufl.edu/ict/documentation/network-infrastructure/vpn/ VPN].
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| − | *
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| − | * To start a GUI application go to [https://ood.rc.ufl.edu https://ood.rc.ufl.edu] and choose the application you would like to use, for example HiPerGator Desktop is a linux GUI.
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| − | **
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| − | ** To start a Jupyter Notebook with OOD, select the “Jupyter Notebook” application server under the “Interactive Applications” tab on the main dashboard. Specify the resources you need in the resource request and click “Launch” at the bottom of the form. Once your job starts, click “Connect to Jupyter” to start your Notebook.
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| − | *
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| − | * To start a Jupyter Notebook go to [http://jhub.rc.ufl.edu http://jhub.rc.ufl.edu] and select the resources you need. This JupyterHub server has preset resource options.
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| − | **
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| − | ** Jupyterhub and OutOfMemory (OOM) – if your Notebook stops responding it might be an indication of the job running out of memory. Currently this does not produce an error message. You can check your <code>/home/<user>/</code>jupyter slurm spawner logs to be sure. You will need to restart the job with additional RAM.
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| − | *
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| − | * To start a Galaxy instance go to [https://galaxy.rc.ufl.edu/ https://galaxy.rc.ufl.edu/]. Galaxy is a web-based framework for accessible, reproducible, and transparent biological computing.
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| − | </div>
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| − | </div>
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| − |
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| − | ===Invalid Password===
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| − | If you have forgotten your password or need to change it, use the links below to set a new one:
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| − |
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| − | [https://my.ufl.edu/ps/signon.html Change or Reset Password]
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| − |
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| − | '''NOTE''': Research Computing now uses Gatorlink Authentication for all passwords. Please use the UF Gatorlink password system for all password issues.
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| − |
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| − | ==Data Management==
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| − |
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| − | ===Transferring Data===
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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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| − |
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| − | ====SFTP====
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| − | SFTP, or secure file transfer, works well for small to medium data transfers and is appropriate for both small and large data files.
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| − |
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| − | If you would like to use a Graphical User Interface secure file transfer client we recommend:
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| − | * <s>[https://filezilla-project.org/download.php?show_all=1 FileZilla] for Windows or MacOS X.</s>
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| − | : The FileZilla installer contains adware/malware and probably should be avoided.
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| − | * [http://winscp.net/eng/index.php WinSCP] for Windows.
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| − | * [http://cyberduck.io/ Cyberduck] for MacOS X and Windows.
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| − |
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| − | After you have chosen and downloaded a client, configure the client to connect to <code>hpg.rc.ufl.edu</code>, specifying port number 22. Use your username and password to log in.
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| − |
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| − | ====Rsync====
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| − | If you prefer to use the command-line or to get maximum efficiency from your data transfers Rsync, which is an incremental file transfer utility that minimizes network usage, is a good choice. It does so by transmitting only the differences between local and remote files rather than transmitting complete files every time a sync is run as SFTP does. Rsync is best used for tasks like synchronizing files stored across multiple subdirectories, or updating large data sets. It works well both for small and large files. [[Rsync|See the Rsync page]] for instructions on using rsync.
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| − |
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| − | ===Globus===
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| − | Globus is a high-performance 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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| − |
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| − | ===Samba===
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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. UFRC Samba setup does not provide high performance, so try to use it sparingly and for smaller files, like job scripts or analysis reports to be copied to your local 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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| − |
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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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| − |
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| − | ===Automounted Paths===
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| − | Note: NFS-based storage on our systems are typically automounted, which means they are dynamically mounted only when users are actually accessing them. For example if you have an invested folder as /orange/smith, to access it you will have to specifically type in the full path of "/orange/smith" to be able to see the contents and access them. Directly browsing /orange will not show the smith sub-folder unless someone else is using it coincidentally. Automounted folders are pretty common on the systems, they include /orange, /bio, /rlts and even /home etc.
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| − |
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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 traditional 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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| − |
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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 afterward. 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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| − |
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| − | ==Computation==
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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:
| + | =Getting help= |
| − | <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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| − | module load <module_name>
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| − | </pre>
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| − | | |
| − | In Jupyter Notebooks, kernels are available with our most popular software stacks. If you are unable to find what you need or would like software installed, please fill out a [https://www.rc.ufl.edu/help/support-requests/ help request].
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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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| − | | |
| − | There are some useful commands and utilities in a [[UFRC_environment_module|'ufrc' environment module]] in addition to installed applications.
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| − | | |
| − | ===Interactive Testing or Development===
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| − | You don't always have to use the SLURM scheduler. When all you need is a quick shell session to run a command or two, write and/or test a job script, or compile some code use [[Development_and_Testing|SLURM Dev Sessions]].
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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 an 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 computational jobs===
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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 an 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 the login nodes accessed via hpg.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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| − | | |
| − | ====Managing Cores and Memory====
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| − | See [[Account and QOS limits under SLURM]] for the main documentation on efficient management of computational resources.
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| − | | |
| − | The amount of resources within an investment is calculated in NCU (Normalized Computing Units), which correspond to 1 CPU core and about 3.5GB of memory for each NCU purchased. CPUs (cores) and RAM are allocated to jobs independently as requested by your job script.
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| − | | |
| − | Your group's investment can run out of **cores** (SLURM may show <code>QOSGrpCpuLimit</code> in the reason a job is pending) OR **memory** (SLURM may show <code>QOSGrpMemLimit</code> in the reason a job is pending) depending on current use by running jobs.
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| − | The majority of HiPerGator nodes have the same ratio of about 4 GB of RAM per core, which, after accounting for the operating system and system services, leaves about 3.5 GB usable for jobs; hence the ratio of 1 core and 3.5GB RAM per NCU.
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| − | | |
| − | Most HiPerGator nodes have 32 cores and 128 GB RAM (~30,000 cores in the newer part of the cluster) or 64 cores and 256 GB RAM (~16,000 cores in the older part of the cluster). The [[Large-Memory SMP Servers|bigmem]] nodes and the newer Skylake nodes have a higher ratio of 16 GB/core and 6 GB/core, respectively. See [[Available_Node_Features]] for the exact data on resources available on all types of nodes on HiPerGator.
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| − | | |
| − | You must specify both the number of cores and the amount of RAM needed in the job script for SLURM with the <code>--mem</code> (total job memory) or <code>--mem-per-cpu</code> (per-core memory) options. Otherwise, the job will be assigned the default 600mb of memory.
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| − |
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| − | If you need more than 128 GB of RAM, you can only run on the older nodes, which have 256 GB of RAM, or on the bigmem nodes, which have up to 1.5 TB of RAM.
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| − | | |
| − | See [[Account and QOS limits under SLURM]] for an extensive explanation of QOS and SLURM account use.
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| − | | |
| − | ==Getting help==
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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]. | | 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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| − | ==Visual 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]]
| |
