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>
Welcome to the <span class="plainlinks">[http://www.ufl.edu/ University of Florida] Research Computing Wiki. The information here augments what is found on our [http://www.hpc.ufl.edu web site] with information we think is best provided in a less formal and official context. It is used for information that changes rapidly and might become quickly dated or incorrect on the web site. While there is good and helpful information here, you ''will'' find text that has not been proofed to the same standards that we try to maintain on our web site. We hope you find it helpful.</span>
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<br>
=== Getting Started ===
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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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{| cellspacing="0" cellpadding="5"
|-
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|- valign="top"
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| width="50%" |
* [[Getting Started]]
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{| width="100%"
* [[Moab Command Summary]]
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| style="width: 7%; vertical-align: top" | [[Image:Setup.png|frameless|upright=0.2]]
*[[Non_Batch-System_Resources|Non-Batch System Resources]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">FOR NEW USERS</h1>
| scope="col" width="150" |
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Guides to get you started with HPG, and best practices!
* [[Mailing Lists]]
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<hr style="margin: 4px 0" />
* [[Events_Calendar]]
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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>
* [[Training]]
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|}
| scope="col" width="150" |
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* [[Password | Changing your Password]]
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{| width="100%"
* <span class="plainlinks">[http://support.rc.ufl.edu Open a Support Request]</span>
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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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|}
  
=== Software and Libraries ===
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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%"
* [[Installed Software]]
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| style="width: 7%; vertical-align: top" | [[Image:Question.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">HELP</h1>
* [[Modules|Environment Modules System]]
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Resources to ask questions, get support, or communicate directly.
| scope="col" width="150" |
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<hr style="margin: 4px 0" />
* [[CUDA|GPUs and CUDA]]
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<span style="font-size: 12pt">'''[[Get_Help|How To Get Help]]''' | [[AI Help|AI Help]] | [[FAQ]] | <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span></span>
 
|}
 
|}
  
=== 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>
*[[Queues|Queue information]]
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Guides for GUI/web interfaces you can run on HPG.
* [[Torque_Job_Arrays|Job Arrays]]
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<hr style="margin: 4px 0" />
* [[PBS_$TMPDIR|Using TMPDIR Variable]]
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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" |
 
* [[Annotated_PBS_Script|Annotated Job Script Example]]
 
* [[PBS_Directives|Basic PBS Directives]]
 
| scope="col" width="150" |
 
* [[Billed Usage]]
 
* [[Large-Memory_SMP_Servers|Big Memory Queue]]
 
 
|}
 
|}
  
=== 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]]
* [[FileZilla|SFTP Transfers with FileZilla]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SCHEDULER</h1>
| scope="col" width="150" |
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How to schedule and manage jobs and resources on HPG and more SLURM info.
* [[Globus]]
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<hr style="margin: 4px 0" />
* [[GUI Programs|GUI Programs and X11]]
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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>
| scope="col" width="150" |
 
* [[PuTTY|Using PuTTY for SSH]]
 
* [[OwnCloud]]
 
|-
 
 
|}
 
|}
  
=== 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]]
| 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">SOFTWARE AND REFERENCE DATA</h1>
| scope="col" width="150" |  
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View installed programs and tools, how to utilize them, and reference data that they can run.
| scope="col" width="150" |
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<hr style="margin: 4px 0" />
|-
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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>
| scope="col" width="150" |
 
* [[Galaxy|Galaxy Genomics Framework]]
 
* [[R|R (BioConductor)]]
 
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* [[BLASTDB|Blast Databases]]
 
* [[Transfer_NGS_Sequence_Data_to_HPC|Data Transfer]]
 
| scope="col" width="150" |
 
* [[:Category:Bioinformatics|Bioinformatics Software]]
 
* [[Sharing Files]]
 
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|}
 
|}
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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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|}
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__NOTOC__
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__NOEDITSECTION__

Latest revision as of 17:10, 1 December 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 | AI Help | FAQ | Submit a Support Request

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