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Search our client documentation below, optionally filtered by one or more systems.

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Owens, Pitzer, Ruby

Singularity is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.

Owens

HTSlib is a C library used for reading and writing high-throughput sequencing data.

Owens, Pitzer

Relion (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy. 

Owens, Ruby

LAPACK (Linear Algebra PACKage) provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.

Availability and Restrictions

Access

A highly optimized implementation of the BLAS is available on all OSC clusters as part of the Intel Math Kernel Library (MKL). We recommend that you use MKL rather than building the BLAS for yourself. MKL is available to all OSC users.

Owens

FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions

Versions

The following versions of FreeSurfer are available on OSC clusters:

Owens, Pitzer, Ruby

It is now possible to run Docker and Singularity containers on the Ruby, Owens and Pitzer clusters at OSC. Single-node jobs are currently supported, including GPU jobs; MPI jobs are planned for the future.

FSL

Owens

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:

Owens, Pitzer, Ruby

This page outlines a way a professor can set up a file submission system at OSC for his/her classroom project.

Usage for Professor

After connecting to OSC system, professor runs submit_prepare as

Ruby

GPU-BLAST is an accelerated version of the popular NCBI-BLAST (www.ncbi.nlm.nih.gov) that uses general-purpose graphics processing unit (GPU). In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results.

Availability and Restrictions

Versions

The following versions of GPU-BLAST are available on OSC systems:

Pages