Apptainer
Apptainer (formerly Singularity) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.
Cardinal
HTSlib
HTSlib is a C library used for reading and writing high-throughput sequencing data.
RELION
RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
FreeSurfer
FreeSurfer is a software package used to anaylze nueroimaging data.
Availability & Restrictions
Versions
The following versions of FreeSurfer are available on OSC clusters:
FSL
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
Availability and Restrictions
Versions
The following versions of FSL are available on OSC clusters:
VirtualGL
VirtualGL allows OpenGL applications to run with 3D hardware accerlation.
Availability & Restrictions
Versions
The following versions of VirtualGL are available on OSC clusters:
Julia
From julialang.org:
"Julia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. Julia’s Base library, largely written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager at a rapid pace. IJulia, a collaboration between the Jupyter and Julia communities, provides a powerful browser-based graphical notebook interface to Julia."
GPU Computing
The OSC GPU Computing environment.
Overview of File Systems
OSC has several different file systems where you can create files and directories. The characteristics of those systems and the policies associated with them determine their suitability for any particular purpose. This section describes the characteristics and policies that you should take into consideration in selecting a file system to use.
HOWTO: Use NFSv4 ACL
This document shows you how to use the NFSv4 ACL permissions system. An ACL (access control list) is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certian file or directory by user or group. NFSv4 ACLs provide more specific options than typical POSIX read/write/execute permissions used in most systems.
These commands are useful for managing ACLs in the dir locations of /users/<project-code>.
Understanding NFSv4 ACL
This is an example of an NFSv4 ACL
