Cardinal

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."

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.

The various file systems are described in subsequent sections.

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

Run STAR-CCM+ to STAR-CCM+ Coupling

This documentation is to discuss how to run STAR-CCM+ to STAR-CCM+ Coupling simulation in batch job at OSC. The following example demonstrates the process of using STAR-CCM+ version 11.02.010 on Cardinal. Depending on the version of STAR-CCM+ and cluster you work on, there mighe be some differences from the example. Feel free to contact OSC Help if you have any questions. 

Darshan

Darshan is a lightweight "scalable HPC I/O characterization tool".  It is intended to profile I/O by emitting log files to a consistent log location for systems administrators, and also provides scripts to create summary PDFs to characterize I/O in MPI-based programs.

Availability and Restrictions

Versions

The following versions of Darshan are available on OSC clusters:

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