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Ascend, Cardinal, Pitzer
HTSlib is a C library used for reading and writing high-throughput sequencing data.
Ascend, 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.
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.
Pitzer
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.
Ascend, Cardinal, Pitzer
FreeSurfer is a software package used to anaylze nueroimaging data.
Availability & Restrictions
Versions
The following versions of FreeSurfer are available on OSC clusters:
Ascend, Cardinal, Pitzer
It is now possible to run Docker and Apptainer/Singularity containers on all clusters at OSC. Single-node jobs are currently supported, including GPU jobs; MPI jobs are planned for the future.
Cardinal, Pitzer
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
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
Ascend, Cardinal, Pitzer
VirtualGL allows OpenGL applications to run with 3D hardware accerlation.
Availability & Restrictions
Versions
The following versions of VirtualGL are available on OSC clusters:
Ascend, Cardinal, Pitzer
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."
