Difference between revisions of "UFRC Help and Documentation"

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[[Category:Docs]]
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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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<br>
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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=== Getting Started ===
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{| cellspacing="0" cellpadding="5"
{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #FF4A00; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"  
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|- valign="top"
|-
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| width="50%" |
| scope="col" width="150" |
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{| width="100%"
* [[Getting Started ]]
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| style="width: 7%; vertical-align: top" | [[Image:Setup.png|frameless|upright=0.2]]
* [[Mailing Lists]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">FOR NEW USERS</h1>
* [[New user training]]
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Guides to get you started with HPG, and best practices!
* [[Training|Training, Events and How-To Videos]]
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<hr style="margin: 4px 0" />
| scope="col" width="150" |
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<span style="font-size: 12pt">'''[[Getting Started ]]''' | [[Training Videos]] | [[Trainings|Trainings & Events]] | [[Development_and_Testing|Interactive Development and Testing]] | [[Storage|Practical Storage Use]] </span>
* [[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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{| width="100%"
* [[Blocked Accounts]]
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| style="width: 7%; vertical-align: top" | [[Image:Access.png|frameless|upright=0.2]]
| scope="col" width="150" |
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">ACCESS</h1>
* [[SSH Key Creation (Windows)]]
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How to connect to HPG with Duo, authenticate multiple connections, or check account.
* <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span>
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<hr style="margin: 4px 0" />
* <span class="plainlinks">[https://www.rc.ufl.edu/services/procedures/storage/types/ Storage Types and Procedures]</span>
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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>
* [[Storage|Practical Storage Use]]
 
* <span class="plainlinks">[https://www.rc.ufl.edu/services/support/teaching-support/ Teaching Support]</span>
 
|-
 
 
|}
 
|}
  
=== Software and Reference Data===
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|- valign="top"
Use the tools from [[UFRC environment module]] for convenience.
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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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{| width="100%"
| scope="col" width="150" |
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| style="width: 7%; vertical-align: top" | [[Image:Question.png|frameless|upright=0.2]]
* [[Applications|Installed Applications]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">HELP</h1>
* [[Reference Data]]
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Resources to ask questions, get support, or communicate directly.
* [[UFRC_environment_module|HiPerGator Tools]]
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<hr style="margin: 4px 0" />
| scope="col" width="150" |
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<span style="font-size: 12pt">'''[[Get_Help|How To Get Help]]''' | <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span> | [[AI Help|AI Help]] | [[FAQ]]</span>
* [[Modules|Environment Modules System]]
 
* [[Software Development]]
 
* [[AI Support]]
 
| scope="col" width="150" |
 
* [[GPU_Access|GPU Access]]
 
* [[Compilers|Available Compilers]]
 
 
|}
 
|}
  
=== Batch System ===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #FF4A00; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
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{| width="100%"
|-
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| style="width: 7%; vertical-align: top" | [[Image:Inter.png|frameless|upright=0.2]]
| scope="col" width="150" |
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">INTERFACES</h1>
* [[SLURM_Commands|SLURM Commands]]
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Guides for GUI/web interfaces you can run on HPG.
* [[Using_Variables_in_SLURM_Jobs|Using Variables in SLURM]]
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<hr style="margin: 4px 0" />
* [[SLURM_Job_Arrays|SLURM Job Arrays]]
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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>
| scope="col" width="150" |
 
* [[Account_and_QOS_limits_under_SLURM|Account and QOS Limits Under SLURM]]
 
* [[Large-Memory_SMP_Servers|Big Memory Partition]]
 
* [[Available Node Features]]
 
| scope="col" width="150" |
 
* [[Annotated_SLURM_Script|Annotated Job Script Walk-through]]
 
* [[Sample_SLURM_Scripts|Sample SLURM Scripts]]
 
 
|}
 
|}
  
=== Connecting and Data Transfer ===
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|- valign="top"
{| 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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||
| scope="col" width="150" |
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{| width="100%"
* [[Samba Access]]
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| style="width: 7%; vertical-align: top" | [[Image:Scheduler.png|frameless|upright=0.2]]
| scope="col" width="150" |
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SCHEDULER</h1>
* [[Globus]]
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How to schedule and manage jobs and resources on HPG and more SLURM info.
| scope="col" width="150" |
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<hr style="margin: 4px 0" />
* [[Transfer Data]]
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<span style="font-size: 12pt">'''[[SLURM_Commands|SLURM Commands]]''' | [[Account_and_QOS_limits_under_SLURM|Account/QOS Limits Under SLURM]] | [[Available Node Features]] | [[Sample_SLURM_Scripts|Job Script Examples]] | [[SLURM_Job_Arrays|Job Arrays]] | [[GPU_Access|GPU Access]] </span>
|-
 
 
|}
 
|}
  
=== Specific Research Areas ===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #FF4A00; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
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{| width="100%"
|-
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| style="width: 7%; vertical-align: top" | [[Image:Software.png|frameless|upright=0.2]]
| 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>
* [[Biology|Biological Research Computing]]
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View installed programs and tools, how to utilize them, and reference data that they can run.
* [[:Category:Bioinformatics|Bioinformatics Software]]
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<hr style="margin: 4px 0" />
| scope="col" width="150" |
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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>
* [[R|R (BioConductor)]]
 
* [[BLASTDB|Blast Databases]]
 
| scope="col" width="150" |
 
* [[Galaxy|Galaxy Genomics Framework]]
 
|-
 
 
|}
 
|}
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|- valign="top"
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||
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Transfer.png|frameless|upright=0.2]]
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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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How to move different sizes of data to and from HPG.
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<hr style="margin: 4px 0" />
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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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||
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Areas.png|frameless|upright=0.2]]
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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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Highlighted areas of specialization commonly seen with HPG.
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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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|}
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|- valign="top"
 +
|}
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__NOTOC__
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__NOEDITSECTION__

Latest revision as of 19:17, 18 November 2022

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 | Submit a Support Request | AI Help | FAQ

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.


SLURM Commands | Account/QOS Limits Under SLURM | Available Node Features | Job Script Examples | Job Arrays | GPU Access

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