1.
Getting Started
Logging in
Running a Simple HPC Job
The HPC Hardware
The HPC Hardware Layout
HPC Training
2.
PBS
What Resources do my Jobs Need?
Writing PBS Job Scripts
Using qstat
Using qdel
Get Info on the Nodes
Get Info on the Queues
Logging into Other Nodes
Running Array Jobs
PBS Manuals
3.
General Software
Using the Intel Compilers
Using MPI
Perl
Install Perlbrew
Install your own Perl Modules
Python
Python Virtual Environments
Install Miniconda Python
Profiling Python
Singularity
Playing with Singularity
Building Containers
Singularity & PBS
Running Legacy Centos 6 Applications
Definition Files
Important Information
References
Julia
R
Workflow Software
Nextflow
4.
Specific Software
Blast
ddscat
FastQC
GROMACS
Miscellaneous
QIIME 2
5.
GPU Computing
Accessing GPU Nodes
Checking Device Capability
Checking GPU Usage
PBS Job Script for GPUs
6.
Miscellaneous
Reproducible Research
Using SSHFS
X Forwarding
7.
FAQ
SSH Problems
Safe FTP/wget Usage
Converting DOS files to UNIX
Restoring Lost Files
Acknowledgments
8.
NCI
Announcements
More
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