Difference between revisions of "UFRC Help and Documentation"

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Welcome to the <span class="plainlinks">[http://www.ufl.edu/ University of Florida] Research Computing Help and Documentation site. General information, announcements, and purchase request forms are on our [https://www.rc.ufl.edu main web site]. The information here is focused on particular applications, services, and usage examples. [https://support.rc.ufl.edu Provide Feedback].</span>
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Welcome to the <span class="plainlinks">[http://www.ufl.edu/ University of Florida] Research Computing Help and Documentation site. The information here is focused on particular applications, services, and usage examples and complements more general policies and information found on our [https://www.rc.ufl.edu main web site]. It is used for information that changes more frequently and might become quickly dated or incorrect on the web site. This site is edited by individual UFRC staff members. If you find inaccuracies, errors, or omissions on this site please [https://support.rc.ufl.edu let us know].</span>
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<!-- {{Note|Submit a support request at [https://support.rc.ufl.edu https://support.rc.ufl.edu]|warn}} -->
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<!-- {{Note|See an important message about EL7->EL8 migration on HiPerGator at [[Rolling Upgrade from RHEL7 to RHEL8]]|warn}} -->
  
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=[[HiPerGator2.0|HiPerGator 2.0 Information]]=
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=== HiPerGator 2.0 Information ===
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Setup.png|frameless|upright=0.2]]
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*
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">FOR NEW USERS</h1>
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Guides to get you started with HPG, and best practices!
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<span style="font-size: 12pt">'''[[Getting Started ]]''' | [[Training Videos]] | [[Training|Trainings & Events]] | [[Development_and_Testing|Interactive Development and Testing]] | [[Storage|Practical Storage Use]] </span>
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Access.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">ACCESS</h1>
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How to connect to HPG with Duo, authenticate multiple connections, or check account.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Authentication With MFA|Multi-Factor Authentication]]''' | [[SSH Multiplexing]] | [[Using SSH Keys To Access HPG | SSH Keys]] | [[Blocked Accounts]] | [[Federated_Account_Request|Federated Access]] and [[Federated_login|Login]] </span>
 
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=== Getting Started ===
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* [[Getting Started ]]
 
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* [[Mailing Lists]]
 
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* [[Events_Calendar]]
 
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* [[Training]]
 
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* [[SLURM_Commands|SLURM Commands]]
 
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* [[Non_Batch-System_Resources|Non-Batch System Resources]]
 
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* [[Development_and_Testing|Interactive Development and Testing]]
 
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* [[GUI Programs]]
 
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* [[Password | Change your Password]]
 
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* <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Open a Support Request]</span>
 
  
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Question.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">HELP</h1>
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Resources to ask questions, get support, or communicate directly.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Get_Help|How To Get Help]]'''  | [[AI Help]] | [[FAQ]] | <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request] | [[HiPerGator Metrics]] | [[Remote Support]]</span></span>
 
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=== Software and Libraries ===
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{| width="100%"
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|-
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| style="width: 7%; vertical-align: top" | [[Image:Inter.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">INTERFACES</h1>
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* [[Installed Software]]
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Guides for GUI/web interfaces you can run on HPG.
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<hr style="margin: 4px 0" />
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* [[Modules|Environment Modules System]]
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<span style="font-size: 12pt"> '''[[Jupyter_Notebooks| Jupyter (Python, R)]]''' | [[Galaxy|Galaxy Genomics Framework]] | [[Open OnDemand|OnDemand (Matlab, RStudio,...)]] | [[Managing Python environments and Jupyter_kernels | Conda and Jupyter Kernels ]] | [[GUI Programs|Running GUI Apps]] </span>
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* [[GPU_Access|GPU Access]]
 
 
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=== Batch System ===
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|-
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{| width="100%"
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* [[SLURM_Commands|SLURM Commands]]
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| style="width: 7%; vertical-align: top" | [[Image:Scheduler.png|frameless|upright=0.2]]
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* [[PBS2SLURM_Command_Reference|Moab (PBS) to SLURM command reference]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SCHEDULER</h1>
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* [[Using_Variables_in_SLURM_Jobs|Using variables in SLURM]]
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How to schedule and manage jobs and resources on HPG and more SLURM info.
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* [[SLURM_Job_Arrays|SLURM Job Arrays]]
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<span style="font-size: 12pt">'''[[SLURM_Commands|Commands]]''' | [[Account_and_QOS_limits_under_SLURM|Account/QOS Limits]] | [[Available Node Features]] | [[Sample_SLURM_Scripts|Job Script Examples]] | [[SLURM_Job_Arrays|Job Arrays]] | [[GPU_Access|GPU Access]] | [[SLURM_Job_States|Job States]] | [[SLURM Partition Limits|Time Limits]]</span>
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* [[NCU and QOS limits under SLURM]]
 
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* [[GUI_Partition|GUI Partition usage]]
 
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* [[Large-Memory_SMP_Servers|Big Memory Queue]]
 
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* [[Annotated_SLURM_Script|Annotated Job Script Example]]
 
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* [[Sample_SLURM_Scripts|Sample SLURM Scripts]]
 
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* [[Example_SLURM-Parallel-Job-Scripts|SLURM parallel job example script]]
 
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* [[Example_SLURM-GPU-Job-Scripts|SLURM GPU job example script]]
 
 
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=== Connecting and Data Transfer ===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #0021A5; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"  
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|-
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| style="width: 7%; vertical-align: top" | [[Image:Software.png|frameless|upright=0.2]]
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| scope="col" width="150" |
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SOFTWARE AND REFERENCE DATA</h1>
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* [[Samba Access]]
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View installed programs and tools, how to utilize them, and reference data that they can run.
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* [[Transfer Data]]
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<span style="font-size: 12pt">'''[[Applications|Installed Applications]]''' | [[UFRC_environment_module|HiPerGator ufrc Tools]] | [[Modules|Environment Modules System]] | [[Reference Data]] | [[AI Reference Datasets]]</span>
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* [[Globus]]
 
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* [[PuTTY|Using PuTTY for SSH]]
 
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* [[GatorBox]]
 
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=== Specific Research Areas ===
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{| width="100%"
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|-
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| style="width: 7%; vertical-align: top" | [[Image:Transfer.png|frameless|upright=0.2]]
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| width="150" | [[Biology|Biological Research Computing]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">TRANSFER DATA</h1>
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| scope="col" width="150" |  
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How to move different sizes of data to and from HPG.
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<hr style="margin: 4px 0" />
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|-
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<span style="font-size: 12pt">'''[[Transfer Data]]''' | [[Globus]] | [[Samba Access]] | [[Sharing Within A Cluster]] | [[Rsync]] </span>
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|}
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* [[Galaxy|Galaxy Genomics Framework]]
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* [[R|R (BioConductor)]]
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{| width="100%"
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|
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| style="width: 7%; vertical-align: top" | [[Image:Areas.png|frameless|upright=0.2]]
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* [[BLASTDB|Blast Databases]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SPECIFIC RESEARCH AREAS</h1>
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| scope="col" width="150" |
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Highlighted areas of specialization commonly seen with HPG.
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* [[:Category:Bioinformatics|Bioinformatics Software]]
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Biology|Biology]]''' | '''[[Nlp|Natural Language Processing]]''' | '''[[Computer Vision]]''' </span>
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__NOTOC__
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__NOEDITSECTION__

Latest revision as of 14:10, 19 March 2024

Welcome to the University of Florida Research Computing Help and Documentation site. General information, announcements, and purchase request forms are on our main web site. The information here is focused on particular applications, services, and usage examples. Provide Feedback.

Setup.png

FOR NEW USERS

Guides to get you started with HPG, and best practices!

Getting Started | Training Videos | Trainings & Events | Interactive Development and Testing | Practical Storage Use

Access.png

ACCESS

How to connect to HPG with Duo, authenticate multiple connections, or check account.

Multi-Factor Authentication | SSH Multiplexing | SSH Keys | Blocked Accounts | Federated Access and Login

Question.png

HELP

Resources to ask questions, get support, or communicate directly.

How To Get Help | AI Help | FAQ | Submit a Support Request | HiPerGator Metrics | Remote Support

Inter.png

INTERFACES

Guides for GUI/web interfaces you can run on HPG.

Jupyter (Python, R) | Galaxy Genomics Framework | OnDemand (Matlab, RStudio,...) | Conda and Jupyter Kernels | Running GUI Apps

Scheduler.png

SCHEDULER

How to schedule and manage jobs and resources on HPG and more SLURM info.

Commands | Account/QOS Limits | Available Node Features | Job Script Examples | Job Arrays | GPU Access | Job States | Time Limits

Software.png

SOFTWARE AND REFERENCE DATA

View installed programs and tools, how to utilize them, and reference data that they can run.

Installed Applications | HiPerGator ufrc Tools | Environment Modules System | Reference Data | AI Reference Datasets

Transfer.png

TRANSFER DATA

How to move different sizes of data to and from HPG.

Transfer Data | Globus | Samba Access | Sharing Within A Cluster | Rsync

Areas.png

SPECIFIC RESEARCH AREAS

Highlighted areas of specialization commonly seen with HPG.

Biology | Natural Language Processing | Computer Vision


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