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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{| cellspacing="20" cellpadding="0" width="100%"
=== Getting Started ===
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|- valign="top"
{| 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="50%" |
|-
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{| width="100%"
| scope="col" width="150" |
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| style="width: 7%; vertical-align: top" | [[Image:Setup.png|frameless|upright=0.2]]
* [[Getting Started]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">FOR NEW USERS</h1>
* [[Training]]
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Guides to get you started with HPG, and best practices!
* [[Frequently Asked Questions]]
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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|Training, Events, Videos]] | [[New user training]] | [[Development_and_Testing|Interactive Development and Testing]] | [[Storage|Practical Storage Use]] </span>
* [[Getting Help]]
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|}
* [[Mailing Lists]]
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||
| scope="col" width="150" |
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{| width="100%"
* [[Policies]]
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| style="width: 7%; vertical-align: top" | [[Image:Access.png|frameless|upright=0.2]]
* [[Password | Changing your Password]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">ACCESS</h1>
* [[Samba Access]]
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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]] | [[Blocked Accounts]]</span>
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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: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]]''' | <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span> | [[AI Help|AI Help]] | [[FAQ]]</span>
 
|}
 
|}
  
=== System Information ===
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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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{| 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>
* [[Schedulers]]
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Guides for GUI/web interfaces you can run on HPG.
* [[Job Submission Queues]]
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<hr style="margin: 4px 0" />
* [[Sample Scripts | Sample Job Scripts]]
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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" |
 
* [[Cluster Monitoring]]
 
* [[Node Performance]]
 
| scope="col" width="150" |
 
* [[Hardware Testing]]
 
* [[Test Nodes]]
 
 
|}
 
|}
  
=== Software and Libraries ===
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|- valign="top"
{| 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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|-
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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:Scheduler.png|frameless|upright=0.2]]
* [[Modules]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SCHEDULER</h1>
* [[Galaxy]]
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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" />
* [[Command List]]
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<span style="font-size: 12pt">'''[[SLURM_Commands|SLURM Commands]]''' | [[Account_and_QOS_limits_under_SLURM|Account/QOS Limits Under SLURM]] | [[Large-Memory_SMP_Servers|Big Memory Partition]] | [[Available Node Features]] | [[Sample_SLURM_Scripts|SLURM Job Script Examples]] | [[SLURM_Job_Arrays|SLURM Job Arrays]] | [[GPU_Access|GPU Access]] </span>
* [[OpenMP]]
 
* [[OpenMPI]]
 
| scope="col" width="150" |
 
* [[Installing Perl Modules|Installing Perl Modules]]
 
* [[Compilers]]
 
* [[CUDA|CUDA Programming Guides]]
 
 
|}
 
|}
  
=== Specific Research Areas ===
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||
{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #228B22; 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]]
 
* [[BioCluster|Bio Cluster]]
 
|
 
* [[BLASTDB|Blast Databases]]
 
* [[Transfer_NGS_Sequence_Data_to_HPC|Transfer data to HPC]]
 
| scope="col" width="150" |
 
* [[:Category:Bioinformatics|Installed software]]
 
* [[Collaborative Work]]
 
|-
 
 
|}
 
|}
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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]]</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]]</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__

Revision as of 17:14, 22 July 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, Events, Videos | New user training | 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 | Blocked Accounts

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 | Big Memory Partition | Available Node Features | SLURM Job Script Examples | SLURM 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

Areas.png

SPECIFIC RESEARCH AREAS

Highlighted areas of specialization commonly seen with HPG.


Biology | Natural Language Processing