Knowledgebase

High Performance Computing
ABySS
Adding FASTA Databases to Mascot/MaxQuant
Access Odyssey using your SecurID Key Fob or Soft Token
Accessing and using Windows HPC Cluster
Acknowledging Time on Odyssey
Architectural Description of the Odyssey Cluster
ATLAS Computing
Automatic Job Checking and Restart on Odyssey
Available Memory on Odyssey
BayesPhylogenies
Change Your Shell
Cladescan
Compiling and Running C Code on Odyssey
Compiling and Running MPIC/C Code on Odyssey
Compiling and Running MPIC/Fortran Code on Odyssey
Concaterpillar
Connect to the Amazon S3 Storage from Odyssey
Copying Data to and from Odyssey using your Fob
CPU Benchmarks
Customizing Your Environment on Odyssey
Debugging MPI applications with Totalview
Design
Find-n-Replace
Fortran and Mixed Language Codes on Odyssey
General-Use Odyssey Queues
Gnuplot
GNU Science Library
GNU Screen
GPGPU Computing on Odyssey
GraphViz
Interactive use of Odyssey (i.e., not submitting jobs)
How are job priorities within a queue determined?
Hyperthreading and Job Slots
Login/Access to Odyssey
LSF “Tightly Packed” jobs
LSF – Scheduling and Managing Cluster Jobs
LSF Queue Change Questions and Answers
LSF: Sumbit a LSF Job
LSF: Controlling Job Load with LSF Job Groups
LSF: Running MPI Jobs on Odyssey
LSF: Running OpenMP or Threaded Applications
LSF: Running Pre-Installed Software Packages in Batch
LSF: Submitting Lots of Short Jobs (Jobs Array)
LSM Throttling
Mathematica GUI Fonts
Matlab
Migrate
Modules (Software) Available on Odyssey
Modules let you Access Different Software Packages on Odyssey
MPI Codes on Odyssey
MPI Libraries on Odyssey
MPI Python Codes on Odyssey
MrBayes
mrbayes-3.1.2_no_tty_no_redline.patch
Odyssey: The Research Computing Linux Cluster
Odyssey New User Guide
Odyssey in Pictures
Omnetpp
OpenGL libGD on Odyssey
OpenMP Software on Odyssey
python-2.7.1 build notes
qchem
RAxML
RCNX – A GUI (non-text) method of accessing Odyssey
rdiff-backup
Restoring Files in Home Directories
rsync
Running Gadget on Odyssey
Sequencing
Siesta

SLURM
Software for Local Use (FAS License)
Software on Odyssey
Some Comments on OpenGL Rendering of Particles
Stata on Odyssey
TOTALVIEW: Debugging Parallel Applications
Transferring Data
Unix Tips and Tricks
Using SSH ControlMaster for Single Sign-On
Using the Amazon EC2 Cluster with Odyssey
VTK – Visualization Toolkit
Why are my jobs in the SSUSP state?
Windows Cluster (MSHPC)
Windows/Mac X11 Forwarding
X11 and GUI – Graphical / non-text use of Odyssey

Bioinformatics
Sequencing Information
Alignment
Format of Output File
NGS Analysis with R
Summary.htm Details

Scientific Computing
TPP Mascot pipeline workaround

Hardware and Software Purchasing

Storage
Connection Instructions for Labs
Data Security – Information on Storage and Use of Confidential Data (HRCI)
File Systems on Odyssey
Mapping Lab Folders or Home Directories
Mapping to Your User/Lab Data Storage (CIFS)
MassSpec Directory Structure
“RCFS1/DATA” Space for those without Dedicated Lab Space
Research Computing Filesystems

Application Hosting
Affected Websites if RC Storage (NS-960) is Unavailable
FAS Licensed Software for Local Use

Instrument Sign-up
SPINAL Overview – Scientific Instrument Reservations and Billing
SPINAL Usage Guide for Researchers
SPINAL Usage Guide for Laboratory Administrators
SPINAL Expense Code Guide for Laboratory Financial Administrators

openauth
Troubleshooting — Synchronzing Clocks

Research Computing Training

VPN
Connecting to the FAS RC VPN from Linux clients
Odyssey VPN for Wireless/Off-Campus Access to Your Files