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] [http://www.hpc.ufl.edu High Performance Computing Center] Wiki. This site provides documentation for various software applications and hardware configurations provided by the UF HPC Center. Please submit a request in our [http://support.hpc.ufl.edu Support System] or send email to [mailto://support@hpc.ufl.edu HPC support].</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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* [[Getting Started]]
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{| width="100%"
* [[Policies]]
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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>
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Guides to get you started with HPG, and best practices!
* [[Getting Help]]
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<hr style="margin: 4px 0" />
* [[Frequently Asked Questions]]
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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>
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* [[Samba Access]]
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* [[Password | Changing your Password]]
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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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=== System Information ===
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|-
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{| width="100%"
* [[Schedulers]]
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| style="width: 7%; vertical-align: top" | [[Image:Question.png|frameless|upright=0.2]]
* [[Job Submission Queues]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">HELP</h1>
* [[Sample Scripts | Sample Job Scripts]]
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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" />
* [[Cluster Monitoring]]
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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>
* [[Operating Environment]]
 
* [[Node Performance]]
 
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* [[Hardware Testing]]
 
 
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=== Software and Libraries ===
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{| width="100%"
|-
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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>
* [[Installed Software]]
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Guides for GUI/web interfaces you can run on HPG.
* [[Modules]]
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<hr style="margin: 4px 0" />
* [[Galaxy]]
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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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* [[Command List]]
 
* [[OpenMP]]
 
* [[OpenMPI]]
 
| scope="col" width="150" |
 
* [[Installing Perl Modules|Installing Perl Modules]]
 
* [[Compilers]]
 
* [[CUDA|CUDA Programming Guides]]
 
 
|}
 
|}
  
=== Specific Research Areas ===
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|- valign="top"
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|-
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| width="150" | [[Biology|Biological Research Computing]]
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{| width="100%"
| scope="col" width="150" |  
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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>
|-
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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" />
* [[Galaxy|Galaxy Genomics Framework]]
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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>
* [[BioCluster|Bio Cluster]]
 
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* [[BLASTDB|Blast Databases]]
 
* [[Transfer_NGS_Sequence_Data_to_HPC|Transfer data to HPC]]
 
| scope="col" width="150" |
 
* [[:Category:Bioinformatics|Installed software]]
 
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Software.png|frameless|upright=0.2]]
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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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View installed programs and tools, how to utilize them, and reference data that they can run.
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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>
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|}
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|- valign="top"
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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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{| 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 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