Owens

Kallisto

Kallisto is an RNA-seq quantification program. It quantifies abundances of transcripts from RNA-seq data and uses psedoalignment to determine the compatibility of reads with targets, without needing alignment.

Apptainer/Singularity

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

From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."

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. 

We have identified some issues with the RELION installations. For more details, please refere the "Known Issues" section below.

To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on both Owens and Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.

The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.

ROLLING REBOOT OF OWENS CLUSTER STARTING 8:30AM OCT 30

We will have a rolling reboot of Owens starting from 8:30AM on Monday, October 30 2017. This rolling reboot will address recent security vulnerabilities patched by RedHat. This rolling reboot won't affect any running jobs, but users may experience longer queue wait time than usual on the Owens cluster. We apologize for any inconvenience this may cause you. (Note: this was postponed from the 24th.) Please contact oschelp@osc.edu if you have any questions.

ROLLING REBOOTS OF OAKLEY AND RUBY STARTING OCT 9

We will have rolling reboots of Oakley and Ruby clusters starting from 8:30AM on Monday October 9, 2017. A rolling reboot of Owens will be scheduled for a later date. These rolling reboots will address recent security vulnerabilities patched by RedHat. These rolling reboots won't affect any running jobs, but users may experience longer queue wait time than usual on the cluster. We apologize for any inconvenience this may cause you. Please contact oschelp@osc.edu if you have any questions.

LAPACK

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.

Availability and Restrictions

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

FreeSurfer

FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions

Versions

The following versions of FreeSurfer are available on OSC clusters:

Pages