Holland Computing Center
HCC-DOCS
Quickstarts
Setting Up and Using Duo
How to Connect
For Windows Users
For Mac/Linux Users
Using MobaXterm
Changing Your Password
Basic Linux commands
Submitting Jobs
Reusing SSH connections in Linux/Mac
FAQ
Guides
Submitting Jobs
Condor Jobs on HCC
HCC Acknowledgment Credit
Job Dependencies
Monitoring Jobs
Partitions
Available Partitions for Crane
Available Partitions for Rhino
Submitting ANSYS Jobs
Submitting CUDA or OpenACC Jobs
Submitting HTCondor Jobs
Submitting MATLAB Jobs
Submitting R Jobs
Submitting a Job Array
Submitting an Interactive Job
Submitting an MPI Job
Submitting an OpenMP Job
Running Applications
Jupyter Notebooks on Crane
Linux File Permissions
How to setup X11 forwarding
Fortran/C on HCC
Bioinformatics Tools
Alignment Tools
BLAT
Bowtie
Bowtie2
Clustal Omega
TopHat/TopHat2
BLAST
Running BLAST Alignment
Create Local BLAST Database
BWA
Running BWA Commands
Biodata Module
Data Manipulation Tools
SRAtoolkit
BamTools
Running BamTools Commands
SAMtools
Running SAMtools Commands
De Novo Assembly Tools
Oases
Ray
SOAPdenovo2
Trinity
Running Trinity in Multiple Steps
Velvet
Running Velvet with Paired-End Data
Running Velvet with Single-End Data
Running Velvet with Single-End and Paired-End Data
Downloading SRA data from NCBI
Pre-processing Tools
Cutadapt
PRINSEQ
Scythe
Sickle
TagCleaner
QIIME
Reference-Based Assembly Tools
Cufflinks
Tools for Removing/Detecting Redundant Sequences
CAP3
CD-HIT
MPI Jobs on HCC
Allinea Profiling & Debugging Tools
Allinea Performance Reports
BLAST with Allinea Performance Reports
LAMMPS with Allinea Performance Reports
Ray with Allinea Performance Reports
Using Allinea Forge via Reverse Connect
Available Software for Crane
Available Software for Rhino
Compiling Source Code
Compiling an OpenMP Application
DMTCP Checkpointing
Installing Perl modules
Module Commands
Running Gaussian at HCC
Running Matlab Parallel Server
Running OLAM at HCC
Running Theano
Using Anaconda Package Manager
Using Singularity and Docker Containers
Handling Data
Using Rclone for File Transfer
High Speed Data Transfers
Using Attic
Integrating Box with HCC
Using NU's Gitlab instance
Setting up GitLab on HCC Clusters
Data for UNMC Users Only
Preventing File Loss
Using the /common File System
Connecting to CB3 iRODS
Globus Connect
Activating HCC Cluster Endpoints
File Transfers Between Endpoints
File Transfers to and from Personal Workstations
File Sharing
Creating Globus Groups
Globus Command Line Interface
Anvil: HCC's Cloud
Adding SSH Key Pairs
Anvil Instance Types
Available images
Connecting to Linux Instances from Mac
Connecting to Linux Instances from Windows
Connecting to Linux Instances using X2Go
Connecting to Windows Instances
Connecting to the Anvil VPN
Creating SSH key pairs on Mac
Creating SSH key pairs on Windows
Creating an Instance
Creating and attaching a volume
Formatting and mounting a volume in Linux
Formatting and mounting a volume in Windows
Resizing an instance
What are the per-group resources limit?
Sandstone
Events
2018
UNL STAT850, Fall 2018
2017
HCC Users Group
HGRLab Anvil Presentation
June Workshop Series 2017
R for Biologists, March 8, 2017
UNK Linear Algebra, Feb. 28, 2017
UNL STAT Alpha Seminar, Fall 2017
UNL STAT802, Fall 2017
UNL STAT802, Jan. 23rd, 2017
UNL STAT850, Fall 2017
UNL STAT950, Fall 2017
2016
HCC Fall Kickstart 2016
HCC QIIME Workshop 2016
HCC Spring Workshop UNO 2016
Instructions for 5/20/16 Allinea Workshop
UNL Numerical Analysis Class, Aug. 5, 2016
2015
HCC Fall Kickstart 2015
2014
August 2014 UNO Workshop
HCC Bioinformatics Workshop, June 2013
July 2014 Bioinformatics Workshop
October 2014 HCC Workshop - CoE
September 2014 HCC Workshos - EAS
2013
HCC Condor Workshop 2013
HCC MPI Workshop 2013
HCC Matlab Workshop 2013
HCC OSG Workshop, June 2013
HCC Supercomputing Symposium 2013
Supercomputing Mini Workshop 2013
2012
Nebraska Supercomputing Symposium '12
Supercomputing Mini Workshop 2012
The Open Science Grid
A simple example of submitting an HTCondor job
Characteristics of an OSG friendly job
How to submit an OSG job with HTCondor
Using Distributed Environment Modules on OSG
Contact Us
hcc.unl.edu
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Events
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2017
> HCC Users Group
Next Meeting: TBA - Add your email address to the sign in sheet to be notified
March 17th 2017: HCCGo by Derek Weitzel
Avery 108 3 to 4 pm
HCC Users Group
Next Meeting: TBA - Add your email address to the sign in sheet to be notified
March 17th 2017: HCCGo by Derek Weitzel
Avery 108 3 to 4 pm
Speaker Slides
2017
HGRLab Anvil Presentation