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====== Cluster Computing ======

Welcome to the CfN wiki for cluster computing resources.

CfN runs a high-performance computing cluster, consisting of 576 Intel Xeon compute cores with a maximum 62GB RAM per job (possibly extensible), a 10Gb high-speed internal network, over 200TB of RAID-6 high-speed storage, and a tape backup system.

The administrator is Michael Stauffer <admin@cfn.med.upenn.edu>

Please let us know of any issues with this wiki.

===== Searching the wiki =====
You can search the entire wiki (e.g. for an error message you got) in the search box in the upper-right of the window.

**TIP** only search for part of an error message, i.e. parts that seem unique to the error and don't include things like compute node names or filenames.

**TIP** Use quotes to search for a complete phrase, e.g. "memory allocation"
===== TOPICS =====

=== Cluster Specifications ===

[[https://cfn.upenn.edu/resources/resource_cfn.htm | Overview for Cluster for Grant Proposals ]]

===Getting Help===

[[asking_for_help|Click here]]

===Intro Topics===
[[Accounts_and_VPN|Accounts and VPN]] (Getting Started) \\
[[Logging_In|Logging In, Linux Basics, X11 & GUI's]] \\
[[ClusterBasics | Cluster Basics]] (Overview) \\

===Running Jobs===
[[Using_OGS_SGE|Using SGE]] (Running Jobs & Gettin' Stuff Done)\\

===Data===
[[FileAccess | File Transfer & Remote File Access]] \\
[[DataArchving | Backup / Archving / Cold Storage]] (Alternate ways to store data) \\
[[GroupDataDirs| Sharing Data - Read/Write access for other users]]\\
[[HCP_data | HCP Data Set]] \\
[[grad_coeffs|Scanner Gradient Coefficient Files]] \\

===Other Topics===
[[XNAT|XNAT]] \\
[[x2go_Remote_Desktop|x2go Remote Desktop]] (Alternative to X11 for slower connections) \\
[[PACS|PACS]] (Clinical Radiology Image Database) \\
[[build_tools|Building/Compiling Software]]

===Troubleshooting / FAQ===
[[Common_errors|Common Issues & Errors Messages]]\\
[[asking_for_help|Asking the Admins for Help]] \\
[[high_lod_tips|What To Do When the Cluster is Very Busy]]

===Application Details & Tips===
[[Matlab_usage|Matlab]] \\
[[FSL_usage|FSL]] \\
[[SPM_usage|SPM]] \\
[[R_ANTsR_usage|R & ANTsR]] \\
[[MRtrix_usage|MRtrix]] \\
[[gcc_tools|gcc/g++]] \\
[[python|Python]] \\
[[java|Java]]\\

===Billing===
[[Cluster_Billing|Cluster Billing - Methods and Fees]] \\
[[Billing_Report_Archive|Billing Reports]] \\
[[Slot_Usage_Reports|Slot Usage Reports (CPU & Memory Usage)]]

===See Also===
[[http://bkandel.github.io/PICSL_Howto//cluster-usage/|PICSL Cluster - Usage Guide]] (For a different view, **BUT** the details here are different than for CfN).
===== PICSL USERS =====

Welcome PICSL Cluster Users - please see this [[PICSL_Transition_Guide|Transition Guide]] to get started using the CfN cluster, **AND** look through the other pages below.