Difference between revisions of "UFRC Help and Documentation"

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[[Category:Docs]]
 
__NOTOC__
 
__NOTOC__
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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{{Note|[[:News:Latest|The latest HiPerGator News and Announcements]]|news}}
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<!-- {{Note|Interactive Jobs in the GPU partition are limited to 6 hrs|news}} -->
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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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<span>[https://outlook.office365.com/owa/calendar/UFITResearchComputingSupport@uflorida.onmicrosoft.com/bookings/ Book an In-Person or Zoom support appointment.]</span>
 
=== Getting Started ===
 
=== Getting Started ===
 
{| 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;"  
 
{| 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;"  
 
|-
 
|-
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Getting Started]]
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* [[Getting Started ]]
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* [[Quick Start Guide]]
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* [[New user training]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Mailing Lists]]
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* [[Training|Training, Events and How-To Videos]]
* [[Training]]
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* [[Development_and_Testing|Interactive Development and Testing]]
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* [[Storage|Practical Storage Use]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Policies]]
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* [[AI Help|AI Help]]
* [[Password | Changing your Password]]
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* <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span>
* [[Samba Access]]
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* [[Support|All Support Options]]</span>
 
|-
 
|-
 
|}
 
|}
  
=== System Information ===
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=== Interfaces and Access===
 
{| 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;"
 
{| 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;"
 
|-
 
|-
 
| scope="col" width="150" |
 
| scope="col" width="150" |
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* [[Jupyter_Notebooks| Jupyter (Python, R)]]
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* [[Galaxy|Galaxy Genomics Framework]]
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* [[GPU_Access|GPU Access]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Cluster Monitoring]]
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* [[GUI Programs|Running GUI Apps]]
* [[Node Performance]]
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* [[Open OnDemand|OnDemand (Matlab, RStudio,...)]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Hardware Testing]]
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* [[Authentication With MFA|Multi-Factor Authentication]]
* [[Test Nodes]]
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* [[SSH Multiplexing]]
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* [[Blocked Accounts]]
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|-
 
|}
 
|}
  
=== Software and Libraries ===
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=== Scheduler ===
 
{| 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;"
 
{| 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;"
 
|-
 
|-
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Installed Software]]
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* [[SLURM_Commands|SLURM Commands]]
* [[Modules]]
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* [[Account_and_QOS_limits_under_SLURM|Account and QOS Limits Under SLURM]]
* [[Galaxy]]
 
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Moab Command Summary]]
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* [[Large-Memory_SMP_Servers|Big Memory Partition]]
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* [[Available Node Features]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Installing Perl Modules|Installing Perl Modules]]
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* [[Sample_SLURM_Scripts|SLURM Job Script Examples]]
* [[CUDA|GPUs and CUDA]]
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* [[SLURM_Job_Arrays|SLURM Job Arrays]]
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|}
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=== Software and Reference Data===
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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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| scope="col" width="150" |
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* [[Applications|Installed Applications]]
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* [[UFRC_environment_module|HiPerGator ufrc Tools]]
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| scope="col" width="150" |
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* [[Modules|Environment Modules System]]
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| scope="col" width="150" |
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* [[Reference Data]]
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* [[AI Reference Datasets]]
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|-
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|}
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=== Transfer Data ===
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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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|-
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| scope="col" width="150" |
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* [[Transfer Data]]
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| scope="col" width="150" |
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* [[Globus]]
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| scope="col" width="150" |
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* [[Samba Access]]
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|-
 
|}
 
|}
  
 
=== Specific Research Areas ===
 
=== Specific Research Areas ===
{|  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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{|  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;"
 
|-
 
|-
| width="150" | [[Biology|Biological Research Computing]]
 
 
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| scope="col" width="150" |  
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* [[Biology|Biocomputing]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
|-
 
| scope="col" width="150" |
 
* [[Galaxy|Galaxy Genomics Framework]]
 
* [[BioCluster|Bio Cluster]]
 
|
 
* [[BLASTDB|Blast Databases]]
 
* [[Transfer_NGS_Sequence_Data_to_HPC|Data Transfer]]
 
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[:Category:Bioinformatics|Bioinformatics Software]]
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* [[Nlp|Natural Language Processing]]
* [[Sharing Files]]
 
 
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Revision as of 20:27, 7 December 2021


Welcome to the 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 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 let us know.

Book an In-Person or Zoom support appointment.

Getting Started

Interfaces and Access

Scheduler

Software and Reference Data

Transfer Data

Specific Research Areas