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HCC Documentation
Introduction to HPC
Connecting to HCC Clusters
Connecting to HCC Clusters
Creating an Account
Creating an Account
- Changing Your Password
- Setting Up and Using Duo
Handling Data
Handling Data
- Sharing data on Swan
- Data storage
  Data storage
  - Using Scratch
  - NRDSTOR
    
    NRDSTOR
    
    MacOS
    
    Smbclient
    
    Swan
    
    Windows
  - Using NU's Gitlab Instance
    
    Using NU's Gitlab Instance
    
    Setting up GitLab on HCC Clusters
  - Linux File Permissions
  - Using Attic
  - Preventing File Loss
  - Integrating Box with HCC
- Data transfer
  Data transfer
Running Applications
Running Applications
- App specific
  App specific
  - Building LIS
  - Building WRF
  - DMTCP Checkpointing
  - Fortran/C on HCC
  - MPI Jobs on HCC
  - Running Gaussian at HCC
  - Install and Running Matlab CobraToolbox, Gurobi, and IBM ILOG CPLEX
  - Running OLAM at HCC
  - Running Paraview
  - Running PostgreSQL
  - Running SAS on HCC
  - Running Theano
  - Visual Studio Code on HCC resources
  - Allinea profiling and debugging
    
    Allinea profiling and debugging
    
    Using Allinea Forge via Reverse Connect
    
    Allinea performance reports
    
    Allinea performance reports
    
    BLAST with Allinea Performance Reports
    
    LAMMPS with Allinea Performance Reports
    
    Ray with Allinea Performance Reports
  - Bioinformatics tools
    
    Bioinformatics tools
    
    Biodata Module
    
    QIIME
    
    Alignment tools
    
    Alignment tools
    
    BLAT
    
    Bowtie
    
    Bowtie2
    
    Clustal Omega
    
    TopHat/TopHat2
    
    Blast
    
    Blast
    
    Create Local BLAST Database
    
    Running BLAST Alignment
    
    Bwa
    
    Bwa
    
    Running BWA Commands
    
    Data manipulation tools
    
    Data manipulation tools
    
    SRAtoolkit
    
    Bamtools
    
    Bamtools
    
    Running BamTools Commands
    
    Samtools
    
    Samtools
    
    Running SAMtools Commands
    
    De novo assembly tools
    
    De novo assembly tools
    
    Oases
    
    Ray
    
    SOAPdenovo2
    
    Trinity
    
    Trinity
    
    Running Trinity in Multiple Steps
    
    Velvet
    
    Velvet
    
    Running Velvet with Paired-End Data
    
    Running Velvet with Single-End and Paired-End Data
    
    Running Velvet with Single-End Data
    
    Pre processing tools
    
    Pre processing tools
    
    Cutadapt
    
    PRINSEQ
    
    Scythe
    
    Sickle
    
    TagCleaner
    
    Reference based assembly tools
    
    Reference based assembly tools
    
    Cufflinks
    
    Removing detecting redundant sequences
    
    Removing detecting redundant sequences
    
    CAP3
    
    CD-HIT
- Running JupyterLab Notebooks with Slurm
  Running JupyterLab Notebooks with Slurm
- Modules
  Modules
  - Available Software for Swan
- User software
  User software
Submitting Jobs
Submitting Jobs
HCC OnDemand
HCC OnDemand
Anvil: HCC's Cloud
Anvil: HCC's Cloud
NRP
NRP
The OSG Consortium
The OSG Consortium
- Characteristics of an OSG friendly job
FAQ
FAQ
Good HCC Pratices
Good HCC Pratices
- ATTIC Guidelines and Best Practices
Contact Us

Table of contents

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¶

Holland Computing Center | 118 Schorr Center, Lincoln NE 68588

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