HCC-DOCS
Unl r for biologists class march 8 2017
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hcc/hcc-docs
HCC-DOCS
hcc/hcc-docs
HCC Documentation
Introduction to HPC
Connecting to HCC Clusters
Connecting to HCC Clusters
Basic Linux commands
How to setup X11 forwarding
Connecting with MobaXterm
Connecting with PuTTY (Windows)
Reusing SSH connections
Connecting with Terminal
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
Using the /common File System
Preventing File Loss
Integrating Box with HCC
Data transfer
Data transfer
File Transfer with CyberDuck
File Transfer with scp
File Transfer with WinSCP
Globus connect
Globus connect
Activating HCC Cluster Collections
File Transfers Between Collections
File Transfers to and from Personal Workstations
File Sharing
Creating Globus Groups
Globus Command Line Interface
Activating UNL OneDrive on Globus
High Speed Data Transfers
Using Rclone with UNL's OneDrive
Connecting to CB3 iRODS
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
Using R Libraries
Using Anaconda Package Manager
Compiling an OpenMP Application
Using Apptainer and Docker Containers
Installing Perl modules
Submitting Jobs
Submitting Jobs
Creating an Interactive Job
Submitting a Job Array
Submitting GPU Jobs
Submitting an MPI Job
Submitting an OpenMP Job
Job Dependencies
Monitoring Jobs
GPU Monitoring and Optimizing
Partitions
Partitions
Available Partitions for Swan
HCC Acknowledgment Credit
App specific
App specific
Submitting ANSYS Jobs
Submitting MATLAB Jobs
Submitting R Jobs
HCC OnDemand
HCC OnDemand
Connecting to HCC OnDemand
Managing and Transferring Files with HCC OnDemand
Job Management and Submission with HCC OnDemand
Shell Access with HCC OnDemand
Virtual Desktop and Interactive Apps with HCC OnDemand
CryoSPARC Interactive App
Anvil: HCC's Cloud
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 the Anvil VPN
Connecting to Windows Instances
Creating an Instance
Creating and attaching a volume
Creating SSH key pairs on Mac
Creating SSH key pairs on Windows
Formatting and mounting a volume in Linux
Formatting and mounting a volume in Windows
Resizing an instance
Using MySQL instances
What are the per-group resources limit?
NRP
NRP
Quick Start
Basic Kubernetes
GPU Pods
Batch Jobs
Deployments
Storage
JupyterHub Service
The OSG Consortium
The OSG Consortium
Characteristics of an OSG friendly job
FAQ
FAQ
HCC Class Info for Instructors
HCC Class Info for Students
Common Retirement
I have an HCC account, now what?
SSH host keys
Good HCC Pratices
Good HCC Pratices
ATTIC Guidelines and Best Practices
Contact Us
Unl r for biologists class march 8 2017
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