Abaqus
Abaqus is fully migrated from the Owens cluster to the Cardinal cluster on December 17, 2024.
ABAQUS is a finite element analysis program owned and supported by SIMULIA, the Dassault Systèmes brand for Realistic Simulation.
Pitzer
Linaro DDT
Linaro DDT is a graphical debugger for HPC applications. It supports pthreads, OpenMP, or MPI code on CPU, GPU, and MIC based architectures.
Availability & Restrictions
Versions
The Linaro DDT versions currently available at OSC are:
FastQC
FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.
Perl
Perl is a family of programming languages.
Cufflinks
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
Apptainer (formerly Singularity)
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.
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.
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 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.
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 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.
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:
