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] 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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{{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;"  
 
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* [[Getting Started]]
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* [[Getting Started ]]
* [[Moab Command Summary]]
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* [[Quick Start Guide]]
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* [[New user training]]
 
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* [[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]]
* [[Events_Calendar]]
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* [[Storage|Practical Storage Use]]
 
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* [[Password | Changing your Password]]
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* [[AI Help|AI Help]]
* <span class="plainlinks">[http://support.rc.ufl.edu Open a Support Request]</span>
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* <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span>
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* [[Support|All Support Options]]</span>
 
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|-
 
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=== Software and Libraries ===
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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;"
 
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|-
 
|-
 
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| scope="col" width="150" |
* [[Installed Software]]
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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]]
 
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* [[Modules|Environment Modules System]]
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* [[GUI Programs|Running GUI Apps]]
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* [[Open OnDemand|OnDemand (Matlab, RStudio,...)]]
 
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| scope="col" width="150" |
* [[CUDA|GPUs and CUDA]]
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* [[Authentication With MFA|Multi-Factor Authentication]]
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* [[SSH Multiplexing]]
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* [[Blocked Accounts]]
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|-
 
|}
 
|}
  
=== Batch System ===
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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;"
 
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|-
 
|-
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Torque_Job_Arrays|Job Arrays]]
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* [[SLURM_Commands|SLURM Commands]]
* [[PBS_$TMPDIR|Using TMPDIR Variable]]
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* [[Account_and_QOS_limits_under_SLURM|Account and QOS Limits Under SLURM]]
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Annotated_PBS_Script|Annotated Job Script Example]]
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* [[Large-Memory_SMP_Servers|Big Memory Partition]]
* [[PBS_Directives|Basic PBS Directives]]
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* [[Available Node Features]]
 
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* [[Billed Usage]]
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* [[Sample_SLURM_Scripts|SLURM Job Script Examples]]
* [[Large-Memory_SMP_Servers|Big Memory Queue]]
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* [[SLURM_Job_Arrays|SLURM Job Arrays]]
 
|}
 
|}
  
=== Connecting and Data Transfer ===
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=== Software and Reference Data===
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|-
 
|-
 
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| scope="col" width="150" |
* [[Samba Access]]
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* [[Applications|Installed Applications]]
* [[FileZilla|SFTP Transfers with FileZilla]]
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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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* [[Transfer Data]]
 
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* [[Globus]]
 
* [[Globus]]
* [[GUI Programs|GUI Programs and X11]]
 
 
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* [[PuTTY|Using PuTTY for SSH]]
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* [[Samba Access]]
* [[OwnCloud]]
 
 
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|-
 
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|}
  
 
=== Specific Research Areas ===
 
=== Specific Research Areas ===
{|  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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{|  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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* [[Biology|Biocomputing]]
 
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|-
 
 
| scope="col" width="150" |
 
| scope="col" width="150" |
* [[Galaxy|Galaxy Genomics Framework]]
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* [[Nlp|Natural Language Processing]]
* [[R|R (BioConductor)]]
 
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* [[BLASTDB|Blast Databases]]
 
* [[Transfer_NGS_Sequence_Data_to_HPC|Data Transfer]]
 
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* [[:Category:Bioinformatics|Bioinformatics Software]]
 
* [[Sharing Files]]
 
 
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[[Privacy_policy|privacy policy]]
 

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